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<TITLE>BIOSEQ.TXT  -  An Example BIOSEQ File</TITLE>
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<I><A HREF="seqio.html">SEQIO -- A Package for Sequence File I/O</A></I>
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<H1>BIOSEQ.TXT  -  An Example BIOSEQ File</H1>

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#
# bioseq.txt - BIOSEQ entries for various databases (Version 1.2)
#
# This file contains BIOSEQ entries for a number of databases.  Currently,
# there are entries for GenBank, GenPept (part of GenBank), NRFES, NRL3D,
# PIR, PROSITE, REPBASE, SWISS-PROT and UTR (part of NRFES).
#
# To customize it for your installation, go through the entries and for
# each entry:
#      1) Change the root directory from "/databases/..." to the 
#         directory where you have installed that database's files.
#     2a) If one of the choices listed in the entry matches your database
#         file organization, uncomment the file/alias lines (if they
#         have been commented).
#     2b) If your installation differed from the choices listed in the
#         entry, comment out any uncommented lines, add the names of
#         the database's files, and rewrite the aliases.
#      3) Comment out (or change the name of) any index files you don't
#         want to use.  Only include the index files for the identifiers
#         you want the users to be able to access entries by.
#      4) Run idxseq for each of the databases to create the index files.
#
# In this version, only a few databases are given, but my hope is that
# this file could become a canonical list of the databases, their
# ftp/WWW locations or ordering information, and their file structure.
# So, if you administer, or are familiar with, a database which either
# is not included here, is incorrectly given here, or occurs in an ftp
# site, CD-ROM or floppy disk release with another file structure,
# please send e-mail to knight@cs.ucdavis.edu.
#


#
# Virtual BIOSEQ entries used to create and store index files for 
# the NID and PID identifiers  (to give random access to entries
# using the "nid" and "pid" identifiers).
#

&gt;NID
&gt;IdPrefix: nid
&gt;Index: /databases/nididx

&gt;PID
&gt;IdPrefix: pid
&gt;Index: /databases/pididx


#
# The EMBL Nucleotide Sequence Database
#
&gt;EMBL:  /databases/embl
&gt;Name:  EMBL
&gt;IdPrefix: embl
&gt;Index: emblindex
&gt;Format: emblfast
&gt;Alphabet:  DNA
    #
    # EMBL files as found at ftp site ftp.ebi.ac.uk in 
    # /pub/databases/embl/release.
    #
    est?.dat, fun.dat, hum?.dat, inv.dat, mam.dat, org.dat, patent.dat,
    phg.dat, pln.dat, pro.dat, rod.dat, sts.dat, syn.dat, unc.dat
    vrl.dat, vrt.dat

    est:(est?.dat),  est1:(est1.dat),  est2:(est2.dat),  est3:(est3.dat),
    est4:(est4.dat),  est5:(est5.dat),  est6:(est6.dat),  fun:(fun.dat),
    hum:(hum?.dat),  hum1:(hum1.dat),  hum2:(hum2.dat),  inv:(inv.dat),
    mam:(mam.dat),  org:(org.dat),  pat:(patent.dat),  patent:(patent.dat),
    phg:(phg.dat),  pln:(pln.dat),  pri:(pri.dat),  pro:(pro.dat),
    rod:(rod.dat),  sts:(sts.dat),  syn:(syn.dat),  unc:(unc.dat),
    vrl:(vrl.dat),  vrt:(vrt.dat)

   
#
# The ENZYME Database
#
&gt;enzyme:  /databases/enzyme
&gt;Name: ENZYME
&gt;IdPrefix: ec
&gt;Index: ecindex
&gt;Format: EMBL
    #
    # Enzyme files as found at ftp site ncbi.nlm.nih.gov in /repository/enzyme.
    #
    enzyme.dat


#
# The GenBank Flat-File Database
#
&gt;GenBank,gb:  /databases/genbank
&gt;Name:  GenBank
&gt;IdPrefix:  gb
&gt;Index: gbindex
&gt;Format:  gbfast
&gt;Alphabet:  DNA
    #
    # GenBank files as found at ftp site ncbi.nlm.nih.gov in /genbank.
    # Uncomment one of the alternatives for the between-release, daily
    # files (if you have those files).
    # 
    gbbct.seq, gbest?.seq, gbinv.seq, gbmam.seq, gbpat.seq, gbphg.seq
    gbpln.seq, gbpri.seq, gbrna.seq, gbrod.seq, gbsts.seq, gbsyn.seq,
    gbuna.seq, gbvrl.seq, gbvrt.seq

    bct:(gbbct.seq), est:(gbest?.seq), est1:(gbest1.seq), est2:(gbest2.seq)
    est3:(gbest3.seq), est4:(gbest4.seq), est5:(gbest5.seq)
    est6:(gbest6.seq), est7:(gbest7.seq), inv:(gbinv.seq),  mam:(gbmam.seq)
    pat:(gbpat.seq), phg:(gbphg.seq), pln:(gbpln.seq), pri:(gbpri.seq)
    rna:(gbrna.seq), rod:(gbrod.seq), sts:(gbsts.seq), syn:(gbsyn.seq)
    una:(gbuna.seq), vrl:(gbvrl.seq), vrt:(gbvrt.seq)
    ~bct:(gbbct.seq), ~est:(gbest?.seq), ~inv:(gbinv.seq),  ~mam:(gbmam.seq)
    ~pat:(gbpat.seq), ~phg:(gbphg.seq), ~pln:(gbpln.seq),  ~pri:(gbpri.seq)
    ~rna:(gbrna.seq), ~rod:(gbrod.seq), ~sts:(gbsts.seq),  ~syn:(gbsyn.seq)
    ~una:(gbuna.seq), ~vrl:(gbvrl.seq), ~vrt:(gbvrt.seq)

    # daily/gbcu.flat,  daily:(daily/gbcu.flat)
    # daily-nc/nc????.flat,  daily:(daily-nc/nc????.flat)


#
# The GenPept Protein Translation of GenBank coding sequences.
#
&gt;GenPept:  /databases/genbank
&gt;Name:  GenPept
&gt;IdPrefix:  gp
&gt;Index: genpeptindex
&gt;Format:  FASTA
&gt;Alphabet:  Protein
    #
    # GenPept files as found at ftp site ncbi.nlm.nih.gov in /genbank
    #
    genpept.fsa, daily/gpcu.fsa


#
# The Non-Redundant Functionally Equivalent Sequences (NRFES) Database.
#
&gt;NRFES:  /databases/NRFES
&gt;Name:  NRFES
&gt;IdPrefix:  gb
&gt;Index: nrfesindex
&gt;Format:  NBRF
&gt;Alphabet:  DNA
    #
    # NRFES files as found at ftp site ncbi.nlm.nih.gov in /repository/NRFES.
    #
    all_v05/(bcta, inva, mama, orga, phga, plna, pria, roda, vrla, vrta, yeaa)
    cds_v05/(bctc, invc, mamc, orgc, phgc, plnc, pric, rodc, vrlc, vrtc, yeac)
    exo_v05/(inve, mame, orge, plne, prie, rode, vrle, vrte, yeae)
    ivs_v05/(invi, mami, orgi, plni, prii, rodi, vrli, vrti, yeai)

    ~:(bcta, inva, mama, orga, phga, plna, pria, roda, vrla, vrta, yeaa)
    all:(bcta, inva, mama, orga, phga, plna, pria, roda, vrla, vrta, yeaa)
    cds:(bctc, invc, mamc, orgc, phgc, plnc, pric, rodc, vrlc, vrtc, yeac)
    exo:(inve, mame, orge, plne, prie, rode, vrle, vrte, yeae)
    ivs:(invi, mami, orgi, plni, prii, rodi, vrli, vrti, yeai)

    bct:(bcta), inv:(inva), mam:(mama), org:(orga), phg:(phga), pln:(plna)
    pri:(pria), rod:(roda), vrl:(vrla), vrt:(vrta), yea:(yeaa)


#
# The NRL_3D Protein Sequence--Structure Database (a mirror of the PDB
# database in PIR/CODATA file format).
#
&gt;NRL3D:  /databases/pir
&gt;Name:  NRL3D
&gt;IdPrefix:  pdb
&gt;Index: nrl3dindex
&gt;Format:  pirfast
&gt;Alphabet:  Protein
    #
    # NRL_3D files as included in the PIR release found at ftp site
    # ncbi.nlm.nih.gov in /repository/PIR.
    #
    nrl3d.dat


#
# The Protein Information Resource (PIR) Database.
#
&gt;PIR:  /databases/pir
&gt;Name:  PIR
&gt;IdPrefix:  pir
&gt;Index: pirindex
&gt;Format:  pirfast
&gt;Alphabet:  Protein
    #
    # PIR files as found at ftp site ncbi.nlm.nih.gov in /repository/PIR.
    #
    pir1.dat, pir2.dat, pir3.dat pir4.dat
    
    ~1:(pir1.dat), ~2:(pir2.dat), ~3:(pir3.dat), ~4:(pir4.dat)
    ~12:(pir1.dat,pir2.dat), ~13:(pir1.dat,pir3.dat), ~23:(pir2.dat,pir3.dat)
    ~123:(pir1.dat,pir2.dat,pir3.dat)
    

#
# The PROSITE Pattern Database.
#
&gt;PROSITE:  /databases/prosite
&gt;Name:  PROSITE
&gt;IdPrefix:  pros
&gt;Index: prositeindex
&gt;Format: EMBL
    #
    # PROSITE files as found at ftp site ncbi.nlm.nih.gov in
    # /repository/prosite.
    #
    prosite.dat


#
# The REPBASE Repetitive Element Database.
#
&gt;repbase:  /databases/repbase
&gt;Name:  REPBASE
&gt;IdPrefix:  rpb
&gt;Index: repbaseindex
&gt;Format:  EMBL
    #
    # REPBASE files as found at ftp site ncbi.nlm.nih.gov in
    # /repository/repbase.
    #
    MAIN/(B1.rodent, B2.rodent, L1.primate, MIR.mammal, MIR.primate,
          MIR.rodent, MIR2.primate, THE.mammal, THE.primate, THE.rodent,
          THR.human, alu.galago, alu.human, alu.other)
    MER/MER*.pri
    REF/(humrep.ref, invrep.ref, mamrep.ref, plnrep.ref, rodrep.ref,
         simple.ref, vertrep.ref)

    B1:(B1.rodent), B2:(B2.rodent), L1:(L1.primate)
    MIR:(MIR.mammal, MIR.primate, MIR.rodent), MIR2:(MIR2.primate)
    THE:(THE.mammal, THE.primate, THE.rodent), THR:(THR.human)
    alu:(alu.galago, alu.human, alu.other)
    rodent:(B1.rodent, B2.rodent, MIR.rodent),
    rod:(B1.rodent, B2.rodent, MIR.rodent),
    primate:(L1.primate, MIR.primate, MIR2.primate, THE.primate)
    pri:(L1.primate, MIR.primate, MIR2.primate, THE.primate)
    mammal:(MIR.mammal, THE.mammal), mam:(MIR.mammal, THE.mammal)     
    human:(THR.human, alu.human)


#
# The SWISS-PROT Protein Sequence Data Bank.
#
&gt;SWISS-PROT,swissprot,sprot:  /databases/swiss-prot
&gt;Name:  SWISS-PROT
&gt;IdPrefix:  sp
&gt;Index: sprotindex
&gt;Format:  spfast
&gt;Alphabet:  Protein
    #
    # SWISS-PROT files as found at ftp site ncbi.nlm.nih.gov in
    # /repository/swiss-prot.  The ?? match the release number of
    # the database.
    #
    sprot??.dat

    #  updates/new-seq.dat


#
# The UTR Database (UnTRanslated regions of protein coding genes).
# 
&gt;UTR:  /databases/NRFES/utr
&gt;Format: FASTA
&gt;Index: utrindex
&gt;Alphabet: DNA
    #
    # UTR files as included in the NRFES release found at ftp site
    # ncbi.nlm.nih.gov in /repository/NRFES/utr.
    #
    amp_3p, bird_3p, dro_3p, fish_3p, inse_3p, mam_3p, mollu_3p
    mou_3p, nema_3p, prot_3p, rat_3p
    amp_5p, bird_5p, dro_5p, fish_5p, inse_5p, mam_5p, mollu_5p
    mou_5p, nema_5p, prot_5p, rat_5p

    ~_3p:(amp_3p, bird_3p, dro_3p, fish_3p, inse_3p, mam_3p, mollu_3p,
          mou_3p, nema_3p, prot_3p, rat_3p)
    ~_5p:(amp_5p, bird_5p, dro_5p, fish_5p, inse_5p, mam_5p, mollu_5p,
          mou_5p, nema_5p, prot_5p, rat_5p)
    3p:(amp_3p, bird_3p, dro_3p, fish_3p, inse_3p, mam_3p, mollu_3p,
        mou_3p, nema_3p, prot_3p, rat_3p)
    5p:(amp_5p, bird_5p, dro_5p, fish_5p, inse_5p, mam_5p, mollu_5p,
        mou_5p, nema_5p, prot_5p, rat_5p)
    amp:(amp_3p,amp_5p), bird:(bird_3p,bird_5p), dro:(dro_3p,dro_5p)
    fish:(fish_3p,fish_5p), inse:(inse_3p,inse_5p), mam:(mam_3p,mam_5p)
    mollu:(mollu_3p,mollu_5p), mou:(mou_3p,mou_5p), nema:(nema_3p,nema_5p)
    prot:(prot_3p,prot_5p), rat:(rat_3p,rat_5p)
</PRE>

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<ADDRESS> 
<a href="http://wwwcsif.cs.ucdavis.edu/~knight">James R. Knight,</a>
<a href="mailto:knight@cs.ucdavis.edu">knight@cs.ucdavis.edu</a><BR>
June 27, 1996
</ADDRESS>
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